I work for a bank, and everytime someone tries to deposit or cash a cc check we have to sent it to collections the reason why is because it is very hard to collect the funds from the cc company and the whole process can take up to 90 days so I was thinking if the pet store took the check to their bank and the bank sent the check to collections that is why it could had taken that long for them to notify you, but at the same time if they didn't even have the real check but only a copy of it ther is no way that the bank could had taken a copy of a check and deposit it.
I agree with everybody else here that there is something fishy about the whole ordeal.
In the meantime, I'm so glad that you are keeping Maddie and that there is always an angel watching over us.